Israel ISF-DFG: Understanding microscopic mechanisms of the biofilm extracellular matrix formation

• Applicants: Dr. Thomas Pfohl; Professor Vasily Zaburdaev, Ph.D.
• Subject Area: Statistical Physics, Nonlinear Dynamics, Complex Systems, Soft and Fluid Matter, Biological Physics ; Biophysics
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 561112971

Bacterial biofilms are ubiquitous and critical in multiple aspects of human life, from daily health when we brush them off from our teeth or when they help us to digest food, to deadly hospital-acquired infections, and large-scale industrial problems of clogging oil pipes or slowing down cruise ships. One of the key hallmarks of a biofilm is the extracellular matrix (ECM), which is secreted by the aggregating bacteria to encapsulate and make them one whole. The roles played by the ECM in the biofilm are truly multifaceted from providing a mechanical scaffold and conveying resilience to physical and biochemical perturbations, to contributing to biofilm spreading, helping to distribute water, nutrients and metal ions, and generally creating a milieu for biochemical exchange between bacterial cells and their environment. While the ECM has always being recognized as the key biofilm component, yet one can argue that the decades of biofilm research were rather focused on bacterial cells, their phenotypic heterogeneity, gene expression patterns, signaling, and the mechanisms underlying antibiotic resistance. We have recently proposed that bacteria in biofilms create a micromilieu of ECM, water and thereby dissolved metal ions, signaling molecules, nutrients and waste molecules. There is a permanent mechano-physico-chemical crosstalk between the cells and the milieu, which also evolves as the biofilm develops. In general, the extracellular space in biofilms is the place where passive physical processes unfold. Importantly, despite decades of research on bacterial ECM, while its components and responsible genes are relatively well characterized for many bacterial species, the sequential process of ECM formation in the extracellular space is not known to date. The microscopic scale of this process, the difficulties with fluorescent labeling of the players involved, and the inability to look inside of opaque biofilms of standard biofilm lab models made it challenging to study this process until now. In this project, we propose leveraging our expertise in bio-microfluidics, bacterial ECM mechanobiology and biochemistry with theoretical modeling to decipher the chronology and microscopic mechanisms of bacterial ECM formation involving the processes of molecular crowding and liquid-liquid phase separation. In the proposed microfluidic setting, using the versatile B. subtilis biofilm model, we will be able to observe the assembly of the ECM at different degrees of separation from secreting cells at the mesoscopic scale representative of the biofilm microenvironment, allowing the application of a wide range of microscopy and microrheology techniques under highly controlled conditions. Taken together, our study will uncover the hitherto unknown mechano-physico-chemical mechanisms leading to the formation of the ECM – the key cementing component of bacterial biofilms – and thus provide novel insights into the physiology of biofilms.

• DFG Programme: Research Grants
• International Connection: Israel
• Partner Organisation: The Israel Science Foundation
• Cooperation Partner: Professorin Dr. Liraz Chai